[gmx-users] MD of DNA-protein complex AND non-protein inhibitor

jlenz jlenz at zbh.uni-hamburg.de
Sun Feb 3 18:17:06 CET 2008

dear gromacs users,

i used gromacs calculate MD trajectories of protein and DNA  
covalently linked. to do so i applied the AMBER ff ports.
afterwards i used a molecular docking tool to dock small non-protein  
ligands into potential cavities built of the DNA-protein complex.
now i am facing the problem, that i again want to simulate the  
molecular dynamics of the most promising complexes of the protein-DNA  
complex and the ligand but do not know which force field to use.  
additionally how can i set up the parameters for the ligands?

any suggestions would be of great help

thanks in advance


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